annotation | Accessing and modifying information in a 'CoreSet' |
annotation-method | Accessing and modifying information in a 'CoreSet' |
annotation<- | Accessing and modifying information in a 'CoreSet' |
annotation<--method | Accessing and modifying information in a 'CoreSet' |
availableTSets | Return a table of ToxicoSets available for download |
cellInfo | Accessing and modifying information in a 'CoreSet' |
cellInfo-method | Accessing and modifying information in a 'CoreSet' |
cellInfo<- | Accessing and modifying information in a 'CoreSet' |
cellInfo<--method | Accessing and modifying information in a 'CoreSet' |
cellName-method | Accessing and modifying information in a 'CoreSet' |
cellNames | Accessing and modifying information in a 'CoreSet' |
cellNames<- | Accessing and modifying information in a 'CoreSet' |
cellNames<--method | Accessing and modifying information in a 'CoreSet' |
checkTSetStructure | A function to verify the structure of a ToxicoSet |
computeAUC | Computes the AUC for a Drug Dose Viability Curve |
computeIC50 | Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve |
computeICn | Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve |
computeLimmaDiffExpr | Generic method for performing differential expression analysis on an S4 object using the limma package |
computeLimmaDiffExpr-method | Conduct differential expression analysis using the limma R pacakge |
curation | Accessing and modifying information in a 'CoreSet' |
curation-method | Accessing and modifying information in a 'CoreSet' |
curation<- | Accessing and modifying information in a 'CoreSet' |
curation<--method | Accessing and modifying information in a 'CoreSet' |
datasetType | Accessing and modifying information in a 'CoreSet' |
datasetType-method | Accessing and modifying information in a 'CoreSet' |
datasetType<- | Accessing and modifying information in a 'CoreSet' |
datasetType<--method | Accessing and modifying information in a 'CoreSet' |
dateCreated | Accessing and modifying information in a 'CoreSet' |
dateCreated-method | Accessing and modifying information in a 'CoreSet' |
dateCreated<- | Accessing and modifying information in a 'CoreSet' |
dateCreated<--method | Accessing and modifying information in a 'CoreSet' |
dim-method | Get the dimensions of a ToxicoSet |
downloadTSet | Download a ToxicoSet object |
drugGeneResponseCurve | Compares gene expression for a specificed set of features over specific drug dosages vs time |
drugInfo | Accessing and modifying information in a 'CoreSet' |
drugInfo<- | Accessing and modifying information in a 'CoreSet' |
drugNames | Accessing and modifying information in a 'CoreSet' |
drugNames<- | Accessing and modifying information in a 'CoreSet' |
drugPerturbationSig | Drug perturbation analysis |
drugTimeResponseCurve | Compares viabilities at a given dose over different experimental durations |
featureInfo | Accessing and modifying information in a 'CoreSet' |
featureInfo-method | Accessing and modifying information in a 'CoreSet' |
featureInfo<- | Accessing and modifying information in a 'CoreSet' |
featureInfo<--method | Accessing and modifying information in a 'CoreSet' |
fNames | Accessing and modifying information in a 'CoreSet' |
fNames-method | Accessing and modifying information in a 'CoreSet' |
fNames<- | Accessing and modifying information in a 'CoreSet' |
fNames<--method | Accessing and modifying information in a 'CoreSet' |
HCC_sig | HCC_sig dataset |
logLogisticRegression | Fits curves of the form E = E_inf + (1 - E_inf)/(1 + (c/EC50)^HS) to dose-response data points (c, E) given by the user and returns a vector containing estimates for HS, E_inf, and EC50. |
mDataNames | Accessing and modifying information in a 'CoreSet' |
mDataNames-method | Accessing and modifying information in a 'CoreSet' |
mDataNames<- | Accessing and modifying information in a 'CoreSet' |
mDataNames<--method | Accessing and modifying information in a 'CoreSet' |
molecularProfiles | Accessing and modifying information in a 'CoreSet' |
molecularProfiles-method | Accessing and modifying information in a 'CoreSet' |
molecularProfiles<- | Accessing and modifying information in a 'CoreSet' |
molecularProfiles<--method | Accessing and modifying information in a 'CoreSet' |
molecularProfilesSlot | Accessing and modifying information in a 'CoreSet' |
molecularProfilesSlot-method | Accessing and modifying information in a 'CoreSet' |
molecularProfilesSlot<- | Accessing and modifying information in a 'CoreSet' |
molecularProfilesSlot<--method | Accessing and modifying information in a 'CoreSet' |
molecularProfilesSlot<-ToxicoSet-method | Accessing and modifying information in a 'CoreSet' |
moleculerProfilesSlot-method | Accessing and modifying information in a 'CoreSet' |
name | Accessing and modifying information in a 'CoreSet' |
name-method | Accessing and modifying information in a 'CoreSet' |
name<- | Accessing and modifying information in a 'CoreSet' |
name<--method | Accessing and modifying information in a 'CoreSet' |
pertNumber | Accessing and modifying information in a 'CoreSet' |
pertNumber-method | Accessing and modifying information in a 'CoreSet' |
pertNumber<- | Accessing and modifying information in a 'CoreSet' |
pertNumber<--method | Accessing and modifying information in a 'CoreSet' |
phenoInfo | Accessing and modifying information in a 'CoreSet' |
phenoInfo-method | Accessing and modifying information in a 'CoreSet' |
phenoInfo<- | Accessing and modifying information in a 'CoreSet' |
phenoInfo<--method | Accessing and modifying information in a 'CoreSet' |
sampleInfo | Accessing and modifying information in a 'CoreSet' |
sampleInfo-method | Accessing and modifying information in a 'CoreSet' |
sampleInfo<- | Accessing and modifying information in a 'CoreSet' |
sampleInfo<--method | Accessing and modifying information in a 'CoreSet' |
sampleName-method | Accessing and modifying information in a 'CoreSet' |
sampleNames | Accessing and modifying information in a 'CoreSet' |
sampleNames-method | Accessing and modifying information in a 'CoreSet' |
sampleNames<- | Accessing and modifying information in a 'CoreSet' |
sampleNames<--method | Accessing and modifying information in a 'CoreSet' |
sensitivityInfo-method | Accessing and modifying information in a 'CoreSet' |
sensitivityInfo<--method | Accessing and modifying information in a 'CoreSet' |
sensitivityMeasures-method | Accessing and modifying information in a 'CoreSet' |
sensitivityMeasures<--method | Accessing and modifying information in a 'CoreSet' |
sensitivityProfiles-method | Accessing and modifying information in a 'CoreSet' |
sensitivityProfiles<--method | Accessing and modifying information in a 'CoreSet' |
sensitivityRaw-method | Accessing and modifying information in a 'CoreSet' |
sensitivityRaw<--method | Accessing and modifying information in a 'CoreSet' |
sensitivitySlot | Accessing and modifying information in a 'CoreSet' |
sensitivitySlot<- | Accessing and modifying information in a 'CoreSet' |
sensitvityInfo<--method | Accessing and modifying information in a 'CoreSet' |
sensNumber | Accessing and modifying information in a 'CoreSet' |
sensNumber-method | Accessing and modifying information in a 'CoreSet' |
sensNumber<- | Accessing and modifying information in a 'CoreSet' |
sensNumber<--method | Accessing and modifying information in a 'CoreSet' |
show-method | Show a ToxicoSet |
show-method | Show ToxicoGx Signatures |
showSigAnnot | Show the Annotations of a signature object |
subsetTo | A function to subset a ToxicoSet to data containing only specified drugs, cells and genes |
summarizeMolecularProfiles | Takes molecular data from a ToxicoSet, and summarises them into one entry per drug and experimental condition. |
summarizeSensitivityProfiles | Takes the sensitivity data from a ToxicoSet, and summarises them into a drug vs cell line table |
TGGATESsmall | TGGATESsmall dataset |
ToxicoSet | ToxicoSet constructor |
ToxicoSet-accessors | Accessing and modifying information in a 'CoreSet' |
ToxicoSet-class | Class to contain Toxico-genomic Data |
treamentResponse<--method | Accessing and modifying information in a 'CoreSet' |
treatmentInfo | Accessing and modifying information in a 'CoreSet' |
treatmentInfo-method | Accessing and modifying information in a 'CoreSet' |
treatmentInfo<- | Accessing and modifying information in a 'CoreSet' |
treatmentInfo<--method | Accessing and modifying information in a 'CoreSet' |
treatmentNames | Accessing and modifying information in a 'CoreSet' |
treatmentNames-method | Accessing and modifying information in a 'CoreSet' |
treatmentNames<- | Accessing and modifying information in a 'CoreSet' |
treatmentNames<--method | Accessing and modifying information in a 'CoreSet' |
treatmentResponse | Accessing and modifying information in a 'CoreSet' |
treatmentResponse-method | Accessing and modifying information in a 'CoreSet' |
treatmentResponse<- | Accessing and modifying information in a 'CoreSet' |
treatmentResponse<--method | Accessing and modifying information in a 'CoreSet' |
updateObject-method | Update the ToxicoSet class after changes in it struture or API |
.ToxicoSet | Class to contain Toxico-genomic Data |
[-method | '[' |